We investigated whether polychlorinated biphenyls (PCBs) partitioning between the dissolved and particulate phases in two high altitude alpine lakes was determined by the quantity, size structure, or composition of suspended particles. Within- and between-lakes differences in water-particulate phase partition coefficient (Kp) were not related to total suspended matter, phytoplankton biomass, or taxonomic composition. Yet, a seasonal relationship between Kp and Kow was detected for both lakes, revealing equilibrium of PCBs partition when lakes were ice covered. On the contrary, PCBs partitioning between particles and water appeared kinetically limited during the open water season. Partition is therefore mainly governed by thermodynamic laws during the ice-covered period, while none of the tested physical or biological parameters seemed to explain the distribution of these particle-reactive contaminants in the open water period. PCBs were always mainly associated with particulate matter, but partitioning within different particulate size-fractions varied between seasons and between years during open water periods. When ice cover is absent, PCBs were mainly adsorbed on microplankton, the largest phytoplanktonic size fraction, which is the least likely to get grazed by pelagic microconsumers.